The amazing Emacs org-mode has myriad uses and features including outlining, note-taking, table management, and publishing to HTML and LaTeX. It’s also a fabulous tool to help make your research reproducible. From Wikipedia (http://en.wikipedia.org/wiki/Reproduc...In 2012, a survey done for Nature found that 47 out of 53 medical research papers on the subject of cancer were irreproducible (http://www.nature.com/nature/journal/... Researchers explained in a 2006 study that, of 249 data sets from American Psychology Association (APA) empirical articles, 73% of contacted authors did not respond with their data (http://www.ncbi.nlm.nih.gov/pubmed/17...) over a 6-month period.

Org-mode allows authors to include their datasets and all programs that were run to generate figures and text. Included files can be used to facilitate version control. While there are limits to this approach—including data generation and software versioning—it represents a big advance in reproducibility and one which has not yet been widely adopted.